The recent scale-up of efforts to complete the sequence of the human genome is producing ever-increasing amounts of unannotated DNA sequence. Computational methods for recognizing coding sequences in genomic DNA, gene prediction programs coupled with similarity searches in protein and cDNA databases, are well established and capable of detecting the majority of genes. However, identifying regulatory elements in the 95% of the genome comprised of non-coding sequences is currently a significantly greater and largely unmet challenge. Numerous experimental studies have demonstrated that regulatory elements tend to be evolutionarily conserved among vertebrates (Li et al., Trends Genet. 15:403 (1999)). Thus, cross-species genomic sequence comparisons provide a potential means for identifying these non-coding sequences of biologic import (Hardison et al., Genome Res. 7:959 (1997)).
Extensive studies have focused on understanding the regulation of the five biomedically important cytokine genes clustered at human 5q31. As evidenced by significant sequence differences between orthologous cytokine genes in different mammals (on average ˜50% identity between humans and mice), these genes are rapidly evolving. However, several of the cytokines in this interval, interleukin-4 (IL-4), interleukin-13 (IL-13), and interleukin-5 (IL-5) have physically remained in close proximity to each other in all species studied to date. This observation, coupled with the fact that IL-4, IL-13, and IL-5 are coordinately co-activated in T helper 2-type (TH2) cells (Abbas et al., Nature 383:787 (1996)), suggests that the clustering of these genes may be due to commonly shared, as of yet unidentified, cis-regulatory sequences. Studies examining human 5q31 YAC transgenic mice demonstrated that the human IL-4, IL-13 and IL-5 transgenes are appropriately regulated in a site-of-integration-independent manner in murine TH2 cells (Symula et al., Nature Genet. 23:241 (1999)), suggesting that the regulatory elements controlling the expression of these cytokines are conserved in humans and mice. However, regulatory elements, such as locus control regions (LCRs), have been difficult to identify.
Enhanced expression of cytokines has been associated with inflammation, autoimmune disorders, and numerous allergic diseases. It would be desirable to identify regulatory elements that control the production of cytokine genes. By understanding and controlling the production of cytokines, such as IL-4, IL-5, and IL-13, disease states can be improved and treated. Embodiments of the invention meet this and other goals.